dicom-series-to-volume

# dicom_series_to_volume ## Purpose - Used for converting one CT DICOM series folder to a HU NIfTI volume with affine evidence. Not for multi-frame DICOM or clinical use. - Use the wrapper exactly as documented; do not replace the upstream entrypoint with a handwritten implementation. - Manifest I/O: inputs are `dicom_dir`; outputs are `nifti_volume` and `result_json`. ## Instructions - Read `skill_manifest.yaml` before changing arguments, side effects, or validation gates. - Run `scripts/series_to_volume.py` through the documented command below; keep outputs under a caller-provided run directory. - If a host agent exposes `run_script`, use `run_script("scripts/series_to_volume.py", args=[...])`; otherwise run the Bash/Python command shown below. - Check the emitted JSON and the paired `dicom_volume_quality_v1` verifier before treating the run as evidence. ## Available Scripts | Script | Purpose | Arguments | |---|---|---| | `scripts/series_to_volume.py` | Primary entrypoint declared by skill_manifest.yaml. | `PATH_TO_DICOM_DIR [--output OUT.nii.gz]` | ## Prerequisites - Runtime requirements: Python packages listed in `runtime.side_effects.pip_packages`. - Run commands from the repository root unless an existing section below says otherwise. ## Limitations - Single-series only; multi-series input is rejected at preflight. - Multi-frame DICOM (NumberOfFrames > 1 per file) not supported. - Compressed transfer syntaxes (JPEG / JPEG2000 / RLE) not supported. - No voxel reori...